[gmx-users] About cutt-off scheme ..
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 29 15:40:48 CEST 2012
rama david wrote:
> Hi Gromacs friends,
> Thank you justin for your explaination ..
> It is, however, common to compromise
> in this respect, and make the solvent layer somewhat smaller in order to
> reduce the computational
> cost. For efficiency reasons the cut-off with triclinic boxes is more
> restricted. For grid search the
> extra restriction is weak:
> Rc < min(ax; by; cz) (3.5)
> For simple search the extra restriction is stronger:
> Rc <1/2min(ax; by; cz) (3.6)
> So from manual and your answer , should I conclude that -d 1.0 nm
> distance is sufficient ???
> if I using command genbox ..... -ci -nmol ... , the molecule are going
> to put randomly ..
> In that case how to maintain -d .. ???
> I am in these confusion because of following reason .....
> I am try to put max molecule to study there interaction ...
> I run simulation of 4 same molecule keep apart in box
> of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
> 284 )
> force field = gromacs96 53a6
> COM (center of mass) information of molecules
> system size : 1.255 1.577 1.883
> box vectors : 4.000 4.000 4.000 (nm)
> mol1 : 2.057 0.844 0.744
> mol 2 : 2.057 0.844 3.141
> mol 3 : 2.057 3.244 0.744
> mol 4 : 2.057 3.244 3.141
> (Four molecule are kept at the four corner of square
> of each side 2.4 nm
> four molecule are catenated in same pdb )
> my md.mdp input is like the ..
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
These settings are not correct for Gromos96 53a6.
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> With command g_mindist -pi
> , select option - 1 (Protein )
> In the index file protein contain information on protein ...
> I got the following result..
> The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
> between atoms 26 and 111
Identify what atoms 26 and 111 are. If they are part of the same molecule, then
yes, you have a problem. It sounds to me like you have 4 separate molecules,
and 2 of them are at a very short distance in the starting configuration. This
is not the same situation as when a molecule sees itself. Whether or not this
is what you want for your simulation setup is up to you.
> Is the simulation is behaving abnormal(I.e simulation is wrong ) or I
> have to select the option system on prompting ??? I am very new to
> these simulation field..
> so all suggestion are appreciable ...
> On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> rama david wrote:
> Hi Gromacs users ,
> as per the link given on gromacs website...
> Introduction to Molecular Dynamics Simulations and Analysis
> <http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/>> - Tutorial for
> performing and analyzing simulations of proteins. Includes
> examples of many of the gromacs analysis tools and addresses a
> number of issues that are commonly raised on the GROMACS user
> list. This tutorial uses GROMACS version 3.3.1 (Tsjerk A.
> editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt
> dodecahedron -d 1.0
> mdp file parameter are as follow ,
> coulombtype = Reaction-Field
> rcoulomb = 1.4
> epsilon_rf = 78
> epsilon_r = 1
> vdw-type = Cut-off
> rvdw = 1.4
> so my query is ..
> As mention in manual ...
> (Page no 14 manual 4.5.4 I am using the Gromacs 4.5.4 )
> *This means that the length of each box vector must exceed the
> length of the macromolecule in the
> direction of that edge plus two times the cut-off radius Rc *.
> Read the next sentence in the manual.
> /In the tutorial -d 1.0 is less than 1.4 ./..
> I noticed that manual version and tutorial gromacs version are
> different ...
> But it raise a lot of confusion for new users like me..
> 1. Is the -d .. should be equal or more than cutt off ???
> Is the -d .. should be equal or more than cutt-off??
> The basic point is that in all simulations you have to avoid the
> same molecule "seeing" itself across a periodic boundary. So in
> reality, you need a periodic distance (which is equivalent to the
> value set with -d, times 2) that exceeds the longest cutoff.
> Assuming the unit cell does not undergo massive shrinking, this
> value is generally pretty stable in an aqueous environment. Setting
> -d 1.0 is common because it creates a 2.0-nm distance between a
> centered solute, which exceeds your cutoff and is sufficient to
> avoid the influence of water ordering, as discussed recently:
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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